/tools/fastx_toolkit/fastx_reverse_complement.xml

https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 63 lines · 45 code · 16 blank · 2 comment · 0 complexity · 0b07d0930a4277fcb7d2d5805feaae6d MD5 · raw file

  1. <tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
  2. <description></description>
  3. <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
  4. <command>zcat -f '$input' | fastx_reverse_complement -v -o $output
  5. #if $input.ext == "fastqsanger":
  6. -Q 33
  7. #end if
  8. </command>
  9. <inputs>
  10. <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
  11. </inputs>
  12. <tests>
  13. <test>
  14. <!-- Reverse-complement a FASTA file -->
  15. <param name="input" value="fastx_rev_comp1.fasta" />
  16. <output name="output" file="fastx_reverse_complement1.out" />
  17. </test>
  18. <test>
  19. <!-- Reverse-complement a FASTQ file -->
  20. <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
  21. <output name="output" file="fastx_reverse_complement2.out" />
  22. </test>
  23. </tests>
  24. <outputs>
  25. <data format="input" name="output" metadata_source="input" />
  26. </outputs>
  27. <help>
  28. **What it does**
  29. This tool reverse-complements each sequence in a library.
  30. If the library is a FASTQ, the quality-scores are also reversed.
  31. --------
  32. **Example**
  33. Input FASTQ file::
  34. @CSHL_1_FC42AGWWWXX:8:1:3:740
  35. TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
  36. +CSHL_1_FC42AGWWWXX:8:1:3:740
  37. 33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26
  38. Output FASTQ file::
  39. @CSHL_1_FC42AGWWWXX:8:1:3:740
  40. TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
  41. +CSHL_1_FC42AGWWWXX:8:1:3:740
  42. 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33
  43. ------
  44. This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
  45. .. __: http://hannonlab.cshl.edu/fastx_toolkit/
  46. </help>
  47. </tool>